Starting phenix.real_space_refine
on Fri Sep 19 04:33:22 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9he1_52074/09_2025/9he1_52074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9he1_52074/09_2025/9he1_52074.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9he1_52074/09_2025/9he1_52074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9he1_52074/09_2025/9he1_52074.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9he1_52074/09_2025/9he1_52074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9he1_52074/09_2025/9he1_52074.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    7460      2.51       5
     N    2023      2.21       5
     O    2322      1.98       5
     H   11404      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23241
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 12141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 786, 12141
          Classifications: {'peptide': 786}
          Link IDs: {'PTRANS': 29, 'TRANS': 756}
    Chain: "B"
      Number of atoms: 5416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 5416
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 11, 'TRANS': 350}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 844
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 3346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 3346
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1291
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 203
          Classifications: {'peptide': 12}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 11}
  Time building chain proxies: 3.74, per 1000 atoms: 0.16
  Number of scatterers: 23241
  At special positions: 0
  Unit cell: (139.656, 122.958, 137.379, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O    2322      8.00
     N    2023      7.00
     C    7460      6.00
     H   11404      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 774.1 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2766

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 17 sheets defined
      23.4% alpha, 29.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 3.837A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 233
      removed outlier: 3.668A  pdb=" N   ARG A 233 " --> pdb=" O   TYR A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 4.462A  pdb=" N   GLN A 286 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LEU A 287 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 314
      removed outlier: 3.627A  pdb=" N   VAL A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.917A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.096A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.848A  pdb=" N   GLY A 451 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 553
      removed outlier: 3.712A  pdb=" N   TRP A 546 " --> pdb=" O   GLN A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 730
      removed outlier: 3.574A  pdb=" N   TYR A 729 " --> pdb=" O   SER A 726 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA A 730 " --> pdb=" O   ASP A 727 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 726 through 730'
    Processing helix  chain 'C' and resid 32 through 39
      removed outlier: 3.957A  pdb=" N   SER C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLY C  37 " --> pdb=" O   ARG C  33 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ASP C  38 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLU C  39 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 32 through 39'
    Processing helix  chain 'D' and resid 31 through 46
    Processing helix  chain 'D' and resid 48 through 62
      removed outlier: 3.754A  pdb=" N   ILE D  52 " --> pdb=" O   TRP D  48 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   THR D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLN D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 105 through 121
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
      removed outlier: 3.588A  pdb=" N   PHE D 169 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
      removed outlier: 3.684A  pdb=" N   VAL D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 213
      removed outlier: 3.691A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 225
    Processing helix  chain 'D' and resid 227 through 240
    Processing helix  chain 'E' and resid 41 through 45
    Processing helix  chain 'E' and resid 51 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 7.470A  pdb=" N   HIS A  30 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   VAL A  88 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLU A  32 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   GLU A  90 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.413A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.822A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER B 193 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295
      removed outlier: 4.180A  pdb=" N   GLU A 294 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   VAL A 335 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY A 270 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 341 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA A 343 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 7.792A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 805
      removed outlier: 3.893A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY A 636 " --> pdb=" O   MET A 711 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674
      removed outlier: 4.894A  pdb=" N   ALA A 672 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 44 through 50
      removed outlier: 4.647A  pdb=" N   THR B  46 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   THR B 391 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67
      removed outlier: 6.781A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118
      removed outlier: 6.066A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL B 141 " --> pdb=" O   ASN B 135 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 6.471A  pdb=" N   LEU B 171 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   THR B 184 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ALA B 173 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203
      removed outlier: 6.535A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA B 218 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 4.001A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 6.744A  pdb=" N   VAL B 305 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR B 318 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ALA B 307 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 5.654A  pdb=" N   ASN B 350 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   PHE B 356 " --> pdb=" O   ASN B 350 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.664A  pdb=" N   PHE E  74 " --> pdb=" O   MET E  64 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35

    536 hydrogen bonds defined for protein.
    1500 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.65

  Time building geometry restraints manager: 3.41 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 11404
        1.03 -     1.23: 1
        1.23 -     1.42: 5238
        1.42 -     1.62: 6796
        1.62 -     1.81: 62
  Bond restraints: 23501
  Sorted by residual:
  bond pdb=" N   LYS A 798 "
       pdb=" CA  LYS A 798 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.14e-02 7.69e+03 6.92e+00
  bond pdb=" N   ASP A 797 "
       pdb=" CA  ASP A 797 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.33e-02 5.65e+03 6.38e+00
  bond pdb=" N   GLY A 796 "
       pdb=" H   GLY A 796 "
    ideal  model  delta    sigma   weight residual
    0.860  0.907 -0.047 2.00e-02 2.50e+03 5.45e+00
  bond pdb=" N   ASP D 134 "
       pdb=" CA  ASP D 134 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.32e-02 5.74e+03 5.12e+00
  bond pdb=" N   GLY A 796 "
       pdb=" CA  GLY A 796 "
    ideal  model  delta    sigma   weight residual
    1.448  1.477 -0.030 1.40e-02 5.10e+03 4.50e+00
  ... (remaining 23496 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 39103
        0.91 -     1.82: 2965
        1.82 -     2.73: 128
        2.73 -     3.64: 53
        3.64 -     4.55: 12
  Bond angle restraints: 42261
  Sorted by residual:
  angle pdb=" CA  ASP D 134 "
        pdb=" CB  ASP D 134 "
        pdb=" CG  ASP D 134 "
      ideal   model   delta    sigma   weight residual
     112.60  116.38   -3.78 1.00e+00 1.00e+00 1.43e+01
  angle pdb=" CA  LYS A 798 "
        pdb=" C   LYS A 798 "
        pdb=" O   LYS A 798 "
      ideal   model   delta    sigma   weight residual
     121.67  117.25    4.42 1.26e+00 6.30e-01 1.23e+01
  angle pdb=" CA  ASP A 797 "
        pdb=" CB  ASP A 797 "
        pdb=" CG  ASP A 797 "
      ideal   model   delta    sigma   weight residual
     112.60  115.88   -3.28 1.00e+00 1.00e+00 1.08e+01
  angle pdb=" CA  ASP A 797 "
        pdb=" C   ASP A 797 "
        pdb=" O   ASP A 797 "
      ideal   model   delta    sigma   weight residual
     120.92  117.95    2.97 1.15e+00 7.56e-01 6.67e+00
  angle pdb=" C   GLY B  53 "
        pdb=" N   SER B  54 "
        pdb=" CA  SER B  54 "
      ideal   model   delta    sigma   weight residual
     121.54  126.09   -4.55 1.91e+00 2.74e-01 5.68e+00
  ... (remaining 42256 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.82: 10445
       15.82 -    31.65: 474
       31.65 -    47.47: 147
       47.47 -    63.29: 75
       63.29 -    79.12: 3
  Dihedral angle restraints: 11144
    sinusoidal: 5995
      harmonic: 5149
  Sorted by residual:
  dihedral pdb=" CA  GLN A 495 "
           pdb=" CB  GLN A 495 "
           pdb=" CG  GLN A 495 "
           pdb=" CD  GLN A 495 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.08  -58.08     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CA  ARG D 166 "
           pdb=" CB  ARG D 166 "
           pdb=" CG  ARG D 166 "
           pdb=" CD  ARG D 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.97   57.97     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" N   CYS A 690 "
           pdb=" CA  CYS A 690 "
           pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.88  -54.12     3      1.50e+01 4.44e-03 9.26e+00
  ... (remaining 11141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1073
       0.028 -    0.055: 474
       0.055 -    0.083: 94
       0.083 -    0.111: 101
       0.111 -    0.139: 45
  Chirality restraints: 1787
  Sorted by residual:
  chirality pdb=" CA  LYS A 798 "
            pdb=" N   LYS A 798 "
            pdb=" C   LYS A 798 "
            pdb=" CB  LYS A 798 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.81e-01
  chirality pdb=" CA  ILE A 601 "
            pdb=" N   ILE A 601 "
            pdb=" C   ILE A 601 "
            pdb=" CB  ILE A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  ILE B 164 "
            pdb=" N   ILE B 164 "
            pdb=" C   ILE B 164 "
            pdb=" CB  ILE B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 1784 not shown)

  Planarity restraints: 3603
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G   7 "    0.115 9.50e-02 1.11e+02   3.84e-02 1.62e+00
        pdb=" NE  ARG G   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG G   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG G   7 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG G   7 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG G   7 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG G   7 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG G   7 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG G   7 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP G   1 "    0.012 2.00e-02 2.50e+03   6.08e-03 1.39e+00
        pdb=" CG  TRP G   1 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TRP G   1 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP G   1 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP G   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP G   1 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP G   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP G   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP G   1 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP G   1 "    0.017 2.00e-02 2.50e+03
        pdb=" HD1 TRP G   1 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 TRP G   1 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE3 TRP G   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" HZ2 TRP G   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" HZ3 TRP G   1 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 154 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO B 155 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 155 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 155 "    0.016 5.00e-02 4.00e+02
  ... (remaining 3600 not shown)

  Histogram of nonbonded interaction distances:
        1.36 -     2.01: 132
        2.01 -     2.66: 31411
        2.66 -     3.31: 63886
        3.31 -     3.95: 80717
        3.95 -     4.60: 126828
  Nonbonded interactions: 302974
  Sorted by model distance:
  nonbonded pdb=" CH2 TRP G   1 "
            pdb=" HB3 ASN G   3 "
     model   vdw
     1.365 2.970
  nonbonded pdb=" CE2 PHE G   5 "
            pdb=" CB  ARG G   7 "
     model   vdw
     1.521 3.450
  nonbonded pdb=" CH2 TRP G   8 "
            pdb=" CB  LYS G  10 "
     model   vdw
     1.522 3.450
  nonbonded pdb=" CH2 TRP G   1 "
            pdb=" CB  ASN G   3 "
     model   vdw
     1.537 3.450
  nonbonded pdb=" CH2 TRP G   8 "
            pdb=" HB3 LYS G  10 "
     model   vdw
     1.626 2.970
  ... (remaining 302969 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             4.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     23.690
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12098  Z= 0.098
  Angle     :  0.425   4.552  16442  Z= 0.236
  Chirality :  0.041   0.139   1787
  Planarity :  0.003   0.050   2164
  Dihedral  :  8.803  65.374   4377
  Min Nonbonded Distance : 1.521

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.76 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.22), residues: 1495
  helix:  3.19 (0.29), residues: 309
  sheet:  0.40 (0.23), residues: 456
  loop : -0.81 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 353 
 TYR   0.010   0.001   TYR D 184 
 PHE   0.009   0.001   PHE E  77 
 TRP   0.015   0.001   TRP G   1 
 HIS   0.001   0.000   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 (12097)
  covalent geometry    : angle       0.42505 (16440)
  SS BOND              : bond        0.00031 (    1)
  SS BOND              : angle       0.08855 (    2)
  hydrogen bonds       : bond        0.11943 (  532)
  hydrogen bonds       : angle       4.83335 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.8629 (ttp) cc_final: 0.8400 (tpp)
REVERT: B   60 TYR cc_start: 0.6365 (t80) cc_final: 0.6160 (t80)
REVERT: B  123 TYR cc_start: 0.4900 (m-80) cc_final: 0.4505 (m-80)
REVERT: B  143 TRP cc_start: 0.3671 (p-90) cc_final: 0.2847 (p-90)
REVERT: B  226 MET cc_start: 0.5497 (tmm) cc_final: 0.4910 (ppp)
  outliers start: 5
  outliers final: 0
  residues processed: 137
  average time/residue: 1.1310
  time to fit residues: 168.5340
Evaluate side-chains
  86 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:   40.0000
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:   50.0000
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 606 ASN
D 102 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.216163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.135519 restraints weight = 55311.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 4.30
r_work: 0.3525 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  12098  Z= 0.222
  Angle     :  0.550   4.753  16442  Z= 0.302
  Chirality :  0.044   0.142   1787
  Planarity :  0.004   0.037   2164
  Dihedral  :  3.900  18.192   1656
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  6.71 %
    Favored  : 91.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.22), residues: 1495
  helix:  2.27 (0.29), residues: 311
  sheet:  0.14 (0.23), residues: 474
  loop : -1.13 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 592 
 TYR   0.019   0.002   TYR D  62 
 PHE   0.022   0.002   PHE A 426 
 TRP   0.012   0.001   TRP G   1 
 HIS   0.005   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (12097)
  covalent geometry    : angle       0.54947 (16440)
  SS BOND              : bond        0.01664 (    1)
  SS BOND              : angle       2.22613 (    2)
  hydrogen bonds       : bond        0.05548 (  532)
  hydrogen bonds       : angle       4.74528 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7817 (mp0)
REVERT: B   60 TYR cc_start: 0.6260 (t80) cc_final: 0.6046 (t80)
REVERT: B  123 TYR cc_start: 0.4852 (m-80) cc_final: 0.4586 (m-80)
REVERT: B  226 MET cc_start: 0.5473 (tmm) cc_final: 0.4801 (ppp)
REVERT: C   41 TYR cc_start: 0.7562 (p90) cc_final: 0.5437 (t80)
  outliers start: 18
  outliers final: 8
  residues processed: 105
  average time/residue: 1.0767
  time to fit residues: 124.7663
Evaluate side-chains
  89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain D residue   56 GLU
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 87 optimal weight:   50.0000
   chunk 93 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 116 optimal weight:    0.0000
   chunk 84 optimal weight:   30.0000
   overall best weight:    1.1390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.217019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.134108 restraints weight = 55488.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.75
r_work: 0.3580 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  12098  Z= 0.121
  Angle     :  0.472   5.725  16442  Z= 0.255
  Chirality :  0.042   0.138   1787
  Planarity :  0.004   0.046   2164
  Dihedral  :  3.772  16.786   1656
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  7.73 %
    Favored  : 91.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.22), residues: 1495
  helix:  2.54 (0.29), residues: 311
  sheet:  0.13 (0.23), residues: 474
  loop : -1.12 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 592 
 TYR   0.013   0.001   TYR D  62 
 PHE   0.012   0.001   PHE E  77 
 TRP   0.006   0.001   TRP A 749 
 HIS   0.003   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (12097)
  covalent geometry    : angle       0.47086 (16440)
  SS BOND              : bond        0.01396 (    1)
  SS BOND              : angle       2.67321 (    2)
  hydrogen bonds       : bond        0.04352 (  532)
  hydrogen bonds       : angle       4.55572 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 TYR cc_start: 0.6271 (t80) cc_final: 0.6068 (t80)
REVERT: B  123 TYR cc_start: 0.4850 (m-80) cc_final: 0.4555 (m-80)
REVERT: B  226 MET cc_start: 0.5435 (tmm) cc_final: 0.4727 (ppp)
REVERT: C   56 MET cc_start: 0.7781 (ptm) cc_final: 0.7540 (ptp)
  outliers start: 11
  outliers final: 6
  residues processed: 94
  average time/residue: 0.9385
  time to fit residues: 97.7470
Evaluate side-chains
  85 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  624 ASP
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 112 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 108 optimal weight:    0.8980
   chunk 146 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:   40.0000
   chunk 7 optimal weight:   20.0000
   chunk 61 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 693 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.216091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.138346 restraints weight = 55408.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 4.50
r_work: 0.3505 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12098  Z= 0.137
  Angle     :  0.481   4.636  16442  Z= 0.261
  Chirality :  0.042   0.136   1787
  Planarity :  0.004   0.042   2164
  Dihedral  :  3.808  16.770   1656
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  7.66 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.22), residues: 1495
  helix:  2.48 (0.29), residues: 311
  sheet:  0.13 (0.23), residues: 472
  loop : -1.18 (0.23), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 592 
 TYR   0.014   0.001   TYR D  62 
 PHE   0.014   0.001   PHE E  77 
 TRP   0.009   0.001   TRP G   1 
 HIS   0.004   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12097)
  covalent geometry    : angle       0.47822 (16440)
  SS BOND              : bond        0.01225 (    1)
  SS BOND              : angle       4.44874 (    2)
  hydrogen bonds       : bond        0.04406 (  532)
  hydrogen bonds       : angle       4.53138 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  777 MET cc_start: 0.8304 (tpt) cc_final: 0.8100 (tpt)
REVERT: B   60 TYR cc_start: 0.6314 (t80) cc_final: 0.6066 (t80)
REVERT: B  123 TYR cc_start: 0.4814 (m-80) cc_final: 0.4532 (m-80)
REVERT: B  226 MET cc_start: 0.5470 (tmm) cc_final: 0.4878 (pmm)
REVERT: C   41 TYR cc_start: 0.7684 (p90) cc_final: 0.5490 (t80)
REVERT: C   56 MET cc_start: 0.7806 (ptm) cc_final: 0.7565 (ptp)
REVERT: E   53 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7438 (tp-100)
  outliers start: 16
  outliers final: 8
  residues processed: 92
  average time/residue: 1.1459
  time to fit residues: 116.6799
Evaluate side-chains
  87 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  589 ASP
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 107 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 120 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 147 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 135 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 94 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 555 HIS
A 693 GLN
D  99 ASN
D 196 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.213760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133895 restraints weight = 55315.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 4.14
r_work: 0.3481 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12098  Z= 0.222
  Angle     :  0.555   6.273  16442  Z= 0.306
  Chirality :  0.044   0.180   1787
  Planarity :  0.005   0.055   2164
  Dihedral  :  4.163  21.724   1656
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.29 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.21), residues: 1495
  helix:  1.96 (0.29), residues: 311
  sheet: -0.09 (0.23), residues: 478
  loop : -1.37 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 197 
 TYR   0.023   0.002   TYR D  62 
 PHE   0.020   0.002   PHE E  77 
 TRP   0.013   0.001   TRP G   1 
 HIS   0.008   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (12097)
  covalent geometry    : angle       0.55428 (16440)
  SS BOND              : bond        0.00907 (    1)
  SS BOND              : angle       2.28925 (    2)
  hydrogen bonds       : bond        0.05555 (  532)
  hydrogen bonds       : angle       4.82211 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7784 (mp0)
REVERT: A  768 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7262 (mtt)
REVERT: B   60 TYR cc_start: 0.6294 (t80) cc_final: 0.6039 (t80)
REVERT: B  123 TYR cc_start: 0.4844 (m-80) cc_final: 0.4600 (m-80)
REVERT: B  226 MET cc_start: 0.5374 (tmm) cc_final: 0.4740 (pmm)
REVERT: C   41 TYR cc_start: 0.7782 (p90) cc_final: 0.5503 (t80)
REVERT: E   28 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.5663 (p90)
  outliers start: 19
  outliers final: 10
  residues processed: 90
  average time/residue: 1.0990
  time to fit residues: 109.5735
Evaluate side-chains
  88 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  746 ASP
Chi-restraints excluded: chain A residue  768 MET
Chi-restraints excluded: chain A residue  797 ASP
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   28 TYR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 144 optimal weight:    1.9990
   chunk 103 optimal weight:   40.0000
   chunk 88 optimal weight:    7.9990
   chunk 115 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 118 optimal weight:    0.6980
   chunk 147 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:   30.0000
   chunk 111 optimal weight:    0.9980
   chunk 24 optimal weight:   20.0000
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.215623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.132844 restraints weight = 55247.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 3.53
r_work: 0.3557 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  12098  Z= 0.121
  Angle     :  0.481   6.926  16442  Z= 0.260
  Chirality :  0.042   0.135   1787
  Planarity :  0.004   0.052   2164
  Dihedral  :  3.924  17.674   1656
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  8.92 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.21), residues: 1495
  helix:  2.35 (0.29), residues: 311
  sheet:  0.04 (0.23), residues: 467
  loop : -1.31 (0.22), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 160 
 TYR   0.015   0.001   TYR A 465 
 PHE   0.010   0.001   PHE A 804 
 TRP   0.006   0.001   TRP G   1 
 HIS   0.004   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (12097)
  covalent geometry    : angle       0.48061 (16440)
  SS BOND              : bond        0.00500 (    1)
  SS BOND              : angle       1.07833 (    2)
  hydrogen bonds       : bond        0.04345 (  532)
  hydrogen bonds       : angle       4.57581 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 GLN cc_start: 0.7587 (pp30) cc_final: 0.7099 (pp30)
REVERT: A  768 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7377 (mtt)
REVERT: A  776 TRP cc_start: 0.7793 (t60) cc_final: 0.7580 (t60)
REVERT: B   60 TYR cc_start: 0.6301 (t80) cc_final: 0.6046 (t80)
REVERT: B  123 TYR cc_start: 0.4774 (m-80) cc_final: 0.4500 (m-80)
REVERT: B  226 MET cc_start: 0.5383 (tmm) cc_final: 0.4850 (pmm)
REVERT: C   41 TYR cc_start: 0.7777 (p90) cc_final: 0.5458 (t80)
REVERT: E   28 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5550 (p90)
REVERT: E   53 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7536 (tp-100)
  outliers start: 17
  outliers final: 9
  residues processed: 93
  average time/residue: 1.0357
  time to fit residues: 107.2478
Evaluate side-chains
  86 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  589 ASP
Chi-restraints excluded: chain A residue  624 ASP
Chi-restraints excluded: chain A residue  768 MET
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   28 TYR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 10 optimal weight:   50.0000
   chunk 134 optimal weight:    1.9990
   chunk 136 optimal weight:    0.0570
   chunk 45 optimal weight:    0.0970
   chunk 68 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 84 optimal weight:   30.0000
   chunk 67 optimal weight:    0.2980
   chunk 31 optimal weight:   10.0000
   chunk 124 optimal weight:    2.9990
   overall best weight:    0.6698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.216438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.132708 restraints weight = 55215.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.87
r_work: 0.3579 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12098  Z= 0.098
  Angle     :  0.467   8.437  16442  Z= 0.250
  Chirality :  0.042   0.133   1787
  Planarity :  0.004   0.050   2164
  Dihedral  :  3.815  17.351   1656
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.31 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.22), residues: 1495
  helix:  2.54 (0.29), residues: 312
  sheet:  0.02 (0.22), residues: 480
  loop : -1.28 (0.23), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.016   0.001   TYR A 465 
 PHE   0.010   0.001   PHE A 804 
 TRP   0.005   0.001   TRP A 749 
 HIS   0.004   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (12097)
  covalent geometry    : angle       0.46495 (16440)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       3.65738 (    2)
  hydrogen bonds       : bond        0.03913 (  532)
  hydrogen bonds       : angle       4.44316 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 GLN cc_start: 0.7549 (pp30) cc_final: 0.7063 (pp30)
REVERT: A  768 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7289 (mtt)
REVERT: A  776 TRP cc_start: 0.7685 (t60) cc_final: 0.7469 (t60)
REVERT: B   60 TYR cc_start: 0.6376 (t80) cc_final: 0.6124 (t80)
REVERT: B  123 TYR cc_start: 0.4759 (m-80) cc_final: 0.4488 (m-80)
REVERT: B  226 MET cc_start: 0.5397 (tmm) cc_final: 0.4879 (pmm)
REVERT: C   41 TYR cc_start: 0.7751 (p90) cc_final: 0.5424 (t80)
REVERT: D  112 ARG cc_start: 0.7539 (ttt-90) cc_final: 0.7287 (ttt-90)
REVERT: E   53 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7473 (tp-100)
  outliers start: 13
  outliers final: 8
  residues processed: 88
  average time/residue: 0.9516
  time to fit residues: 93.0153
Evaluate side-chains
  87 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  624 ASP
Chi-restraints excluded: chain A residue  768 MET
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 130 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 0 optimal weight:   40.0000
   chunk 46 optimal weight:    1.9990
   chunk 140 optimal weight:    0.3980
   chunk 139 optimal weight:    2.9990
   chunk 84 optimal weight:   30.0000
   chunk 12 optimal weight:   20.0000
   chunk 146 optimal weight:    1.9990
   chunk 102 optimal weight:    9.9990
   overall best weight:    1.8788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.214269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.130587 restraints weight = 54468.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 3.74
r_work: 0.3488 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12098  Z= 0.171
  Angle     :  0.513   8.974  16442  Z= 0.278
  Chirality :  0.043   0.137   1787
  Planarity :  0.004   0.054   2164
  Dihedral  :  3.976  18.792   1656
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.47 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.22), residues: 1495
  helix:  2.22 (0.29), residues: 313
  sheet: -0.04 (0.22), residues: 477
  loop : -1.35 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 160 
 TYR   0.019   0.001   TYR D  62 
 PHE   0.015   0.001   PHE E  77 
 TRP   0.008   0.001   TRP G   1 
 HIS   0.006   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (12097)
  covalent geometry    : angle       0.51166 (16440)
  SS BOND              : bond        0.00850 (    1)
  SS BOND              : angle       2.88895 (    2)
  hydrogen bonds       : bond        0.04739 (  532)
  hydrogen bonds       : angle       4.60971 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 GLN cc_start: 0.7570 (pp30) cc_final: 0.7056 (pp30)
REVERT: B   60 TYR cc_start: 0.6356 (t80) cc_final: 0.6100 (t80)
REVERT: B  123 TYR cc_start: 0.4769 (m-80) cc_final: 0.4540 (m-80)
REVERT: B  226 MET cc_start: 0.5439 (tmm) cc_final: 0.4905 (pmm)
REVERT: C   41 TYR cc_start: 0.7762 (p90) cc_final: 0.5391 (t80)
REVERT: E   53 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7439 (tp-100)
  outliers start: 14
  outliers final: 10
  residues processed: 89
  average time/residue: 0.9950
  time to fit residues: 98.3556
Evaluate side-chains
  85 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  589 ASP
Chi-restraints excluded: chain A residue  624 ASP
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 130 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 14 optimal weight:   40.0000
   chunk 9 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0870
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.215838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.133041 restraints weight = 55214.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 3.76
r_work: 0.3547 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12098  Z= 0.104
  Angle     :  0.479  10.438  16442  Z= 0.255
  Chirality :  0.042   0.132   1787
  Planarity :  0.004   0.052   2164
  Dihedral  :  3.834  17.081   1656
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.02 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.22), residues: 1495
  helix:  2.52 (0.29), residues: 311
  sheet: -0.00 (0.22), residues: 479
  loop : -1.30 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G   7 
 TYR   0.016   0.001   TYR A 465 
 PHE   0.010   0.001   PHE A 804 
 TRP   0.006   0.001   TRP A 749 
 HIS   0.004   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (12097)
  covalent geometry    : angle       0.47876 (16440)
  SS BOND              : bond        0.00554 (    1)
  SS BOND              : angle       2.18167 (    2)
  hydrogen bonds       : bond        0.04025 (  532)
  hydrogen bonds       : angle       4.45408 ( 1500)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 GLN cc_start: 0.7562 (pp30) cc_final: 0.7048 (pp30)
REVERT: B   60 TYR cc_start: 0.6368 (t80) cc_final: 0.6116 (t80)
REVERT: B  123 TYR cc_start: 0.4760 (m-80) cc_final: 0.4491 (m-80)
REVERT: B  226 MET cc_start: 0.5413 (tmm) cc_final: 0.4883 (pmm)
REVERT: C   41 TYR cc_start: 0.7674 (p90) cc_final: 0.5376 (t80)
REVERT: D   58 LEU cc_start: 0.6123 (tm) cc_final: 0.5849 (tt)
REVERT: D  112 ARG cc_start: 0.7446 (ttt-90) cc_final: 0.7189 (ttt-90)
REVERT: E   53 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7449 (tp-100)
  outliers start: 11
  outliers final: 10
  residues processed: 87
  average time/residue: 1.0422
  time to fit residues: 100.7565
Evaluate side-chains
  86 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  589 ASP
Chi-restraints excluded: chain A residue  624 ASP
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 112 optimal weight:   20.0000
   chunk 76 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 147 optimal weight:    2.9990
   chunk 113 optimal weight:   20.0000
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.216208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.137750 restraints weight = 54871.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 4.41
r_work: 0.3545 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12098  Z= 0.102
  Angle     :  0.464   8.670  16442  Z= 0.247
  Chirality :  0.042   0.131   1787
  Planarity :  0.004   0.053   2164
  Dihedral  :  3.725  16.702   1656
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.02 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.22), residues: 1495
  helix:  2.68 (0.29), residues: 311
  sheet:  0.03 (0.22), residues: 479
  loop : -1.28 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.015   0.001   TYR A 465 
 PHE   0.009   0.001   PHE A 804 
 TRP   0.007   0.001   TRP B 279 
 HIS   0.004   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (12097)
  covalent geometry    : angle       0.46368 (16440)
  SS BOND              : bond        0.00511 (    1)
  SS BOND              : angle       1.97085 (    2)
  hydrogen bonds       : bond        0.03739 (  532)
  hydrogen bonds       : angle       4.34633 ( 1500)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2990 Ramachandran restraints generated.
    1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 GLN cc_start: 0.7524 (pp30) cc_final: 0.7016 (pp30)
REVERT: B   60 TYR cc_start: 0.6352 (t80) cc_final: 0.6109 (t80)
REVERT: B  123 TYR cc_start: 0.4815 (m-80) cc_final: 0.4526 (m-80)
REVERT: B  226 MET cc_start: 0.5452 (tmm) cc_final: 0.4787 (pmm)
REVERT: C   41 TYR cc_start: 0.7652 (p90) cc_final: 0.5363 (t80)
REVERT: D   48 TRP cc_start: 0.5090 (m100) cc_final: 0.3743 (m-90)
REVERT: D   58 LEU cc_start: 0.6208 (tm) cc_final: 0.5914 (tt)
REVERT: D  112 ARG cc_start: 0.7393 (ttt-90) cc_final: 0.7129 (ttt-90)
REVERT: E   53 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7444 (tp-100)
  outliers start: 9
  outliers final: 9
  residues processed: 92
  average time/residue: 1.0913
  time to fit residues: 110.3779
Evaluate side-chains
  90 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  589 ASP
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 120 optimal weight:    5.9990
   chunk 109 optimal weight:   50.0000
   chunk 106 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 138 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.215197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.132329 restraints weight = 54844.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 3.77
r_work: 0.3510 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12098  Z= 0.137
  Angle     :  0.488  11.142  16442  Z= 0.260
  Chirality :  0.042   0.131   1787
  Planarity :  0.004   0.061   2164
  Dihedral  :  3.783  16.482   1656
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.50 %
    Favored  : 88.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.22), residues: 1495
  helix:  2.53 (0.29), residues: 312
  sheet: -0.02 (0.22), residues: 481
  loop : -1.30 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 160 
 TYR   0.016   0.001   TYR A 465 
 PHE   0.012   0.001   PHE E  77 
 TRP   0.007   0.001   TRP A 776 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12097)
  covalent geometry    : angle       0.48747 (16440)
  SS BOND              : bond        0.00602 (    1)
  SS BOND              : angle       1.95547 (    2)
  hydrogen bonds       : bond        0.04103 (  532)
  hydrogen bonds       : angle       4.40437 ( 1500)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9085.05 seconds
wall clock time: 153 minutes 56.22 seconds (9236.22 seconds total)